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At least 1,153 records · Page 64Linked to original sources
PubMed1990

Opioid peptides in micellar systems: conformational analysis by CD and by one-dimensional and two-dimensional 1H-NMR spectroscopy.

beta-Endorphin has been studied in SDS micelles by one- and two-dimensional nmr spectroscopy (1D and 2D nmr), and to explore the influence of peptide length and composition on the polypeptide structure, the investigation was extended to a number of fragments. The nmr results are compared with those obtained from CD experiments and discussed in terms of a secondary structure that involves the central region of beta-endorphin.

Amino Acid Sequence↗
PubMed2005

One-dimensional polymers based on [{CpMo(CO)2}2(mu,eta2-P2)]: solid-state conformation analysis by NMR spectroscopy and DFT calculations.

Reaction of the complex [{CpMo(CO)2}2(mu,eta2-P2)] (1) with CuI halides leads to the quantitative formation of the novel one-dimensional linear polymers [CuX{Cp2Mo2(CO)4(mu,eta2:eta1:eta1-P2)}](infinity) (X=Cl (4), Br (5), I (6)). The same products 4 and 5 were obtained when 1 was treated with CuCl2 and CuBr2, respectively. The solid-state structures are compared and their remarkable influence on the respective (31)P magic angle spinning (MAS) NMR spectra is interpreted with the help of density functional theory (DFT) calculations on the model compounds [{(CuX)2{Cp2Cr2(CO)4(mu,eta(2):eta1:eta1-P2)}2}3] (X=Cl (4 a), Br (5 a)) in which the molybdenum atoms are replaced by their lighter homologue chromium.

Journal Article↗
PubMed2005

Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis.

A model based on classical concepts is derived to describe the effect of the nitro group on proton chemical shifts. The calculated chemical shifts are then compared to ab initio (GIAO) calculated chemical shifts. The accuracy of the two models is assessed using proton chemical shifts of a set of rigid organic nitro compounds that are fully assigned in CDCl3 at 700 MHz. The two methods are then used to evaluate the accuracy of different popular post-SCF methods (B3LYP and MP2) and molecular mechanics methods (MMX and MMFF94) in calculating the molecular structure of a set of sterically crowded nitro aromatic compounds. Both models perform well on the rigid molecules used as a test set, although when using the GIAO method a general overestimation of the deshielding of protons near the nitro group is observed. The analysis of the sterically crowded molecules shows that the very popular B3LYP/6-31G(d,p) method produces very poor twist angles for these, and that using a larger basis set [6-311++G(2d,p)] gives much more reasonable results. The MP2 calculations, on the other hand, overestimate the twist angles, which for these compounds compensates for the deshielding effect generally observed for protons near electronegative atoms when using the GIAO method at the B3LYP/6-311++G(2d,p) level. The most accurate results are found when the structures are calculated using B3LYP/6-311++G(2d,p) level of theory, and the chemical shifts are calculated using the CHARGE program based on classical models.

Journal Article↗
PubMed1992

Time-resolved fluorescence studies of tryptophan mutants of Escherichia coli glutamine synthetase: conformational analysis of intermediates and transition-state complexes.

Single tryptophan-containing mutants of low adenylylation state Escherichia coli glutamine synthetase have been studied by frequency-domain fluorescence spectroscopy in the presence of various substrates and inhibitors. At pH 6.5, the Mn-bound wild-type enzyme (wild type has two tryptophans/subunit) and the mutant enzymes exhibit heterogeneous fluorescence decay kinetics; the individual tryptophans are adequately described by a triple exponential decay scheme. The recovered lifetime values are 5.9 ns, 2.6 ns, and 0.4 ns for Trp-57 and 5.8 ns, 2.3 ns, and 0.4 ns for Trp-158. These values are nearly identical to the previously reported results at pH 7.5 (Atkins, W.M., Stayton, P.S., & Villafranca, J.J., 1991, Biochemistry 30, 3406-3416). In addition, Trp-57 and Trp-158 both exhibit an ATP-induced increase in the relative fraction of the long lifetime component, whereas only Trp-57 is affected by this ligand at pH 7.5. The transition-state analogue L-methionine-(R,S)-sulfoximine (MSOX) causes a dramatic increase in the fractional intensity of the long lifetime component of Trp-158. This ligand has no effect on the W158S mutant protein and causes a small increase in the fractional intensity of the long lifetime component of the W158F mutant protein. Addition of glutamate to the ATP complex, which affords the gamma-glutamylphosphate-ADP complex, results in the presence of new lifetime components at 7, 3.2, and 0.5 ns for Trp-158, but has no effect on Trp-57. Similar results were obtained when ATP was added to the MSOX complex; Trp-57 exhibits heterogeneous fluorescence decay with lifetimes of 7, 3.5, and 0.8 ns. Decay kinetics of Trp-158 are best fit to a nearly homogeneous decay with a lifetime of 5.5 ns in the MSOX-ATP inactivated complex. These results provide a model for the sequence of structural and dynamic changes that take place at the Trp-57 loop and the central loop (Trp-158) during several intermediate stages of catalysis.

Adenosine Diphosphate↗
PubMed1996

Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly].

The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several decades. Recent advances in the computational methodology of restrained molecular dynamics, used in conjunction with data obtained from two-dimensional 1H NMR spectroscopy, make it a promising method to study peptide and protein structure and function. Several issues, however, need to be addressed in order to assess the validity of this method for its explanatory and predictive value. Among the issues addressed in this study are: the accuracy and generizability of the GROMOS peptide molecular mechanics force field; the effect of inclusion of solvent on the simulations; and the effect of different types of restraining algorithms on the computational results. The decapeptide Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly, which corresponds to the sequence of ACTH1-10, has been synthesized, cyclized, and studied by two-dimensional 1H NMR spectroscopy. Restrained molecular dynamics (RMD) and time-averaged restrained molecular dynamics (TARMD) simulations were carried out on four different distance-geometry starting structures in order to determine and contrast the behavior of cyclic ACTH1-10 in vacuum and in solution. For the RMD simulations, the structures did not fit the NOE data well, even at high values of the restraining potential. The TARMD simulation method, however, was able to give structures that fit the NOE data at high values of the restraining potential. In both cases, inclusion of explicit solvent molecules in the simulation had little effect on the quality of the fit, although it was found to dampen the motion of the cyclic peptide. For both simulation techniques, the number and size of the NOE violations increased as the restraining potential approached zero. This is due, presumably, to inadequacies in the force field. Additional TARMD vacuum-phase simulations, run with a larger memory length or with a larger sampling size (16 additional distance-geometry structures), yielded no significantly different results. The computed data were then analyzed to help explain the sparse NOE data and poor chymotryptic activity of the cyclic peptide. Cyclic ACTH1-10, which contains the functional moieties of the catalytic triad of chymotrypsin, was evaluated as a potential mimic of chymotrypsin by measurement of the rate of hydrolysis of esters of L- and D-phenylalanine. The poor rate of hydrolysis is attributed to the flexibility of the decapeptide, the motion of the side chains, which result in the absence of long-range NOEs, the small size of the macrocycle relative to that of the substrate, and the inappropriate orientation of the Gly, His, and Ser residues. The results demonstrate the utility of this method in computer-aided molecular design of cyclic peptides and suggest structural modifications for future work based on a larger and more rigid peptide framework.

Adrenocorticotropic Hormone↗
PubMed1986

pH dependent insertion of a diphtheria toxin B fragment peptide into the lipid membrane: a conformational analysis.

A peptide of diphtheria toxin B fragment (residues 147-266) has been shown to induce pore formation in lipid bilayer membranes at low pH. Such an effect was obtained at a much lower extent or not at all at pH = 7. The region localized between residues 225 and 246 is highly hydrophobic (27.3% polarity) and characterized by a high concentration of proline residues. Since proline cis-trans isomerization is highly sensitive to the pH of the medium, we investigated the capability of the cis and trans isomers to penetrate into the lipid matrix. Obviously, the cis-trans isomerization of proline 242 and 245, assumed to be imposed by a low pH, uncovers the hydrophobic region and induces its insertion into a lipid layer of dipalmitoylphosphatidylcholine. The lipid matrix destabilization resulting from this process could promote the penetration into the lipid bilayer of an amphipatic structure (153-178) similar to the transverse lipid associating domains of membrane proteins.

Diphtheria Toxin↗
PubMed1975

Conformational analysis of phosphatidylethanol-amine in multilayers by infrared dichroism.

Built-up films of L-alpha-dipalmitoyl phosphatidylethanolamine were prepared. Infrared dichroism was measured for the sample and analysed by a new method. This method has been developed for the determination of the directions of transition moments in a film sample, in which there is an axis of symmetry of perpendicular to the film plane. The directions of transition moments were determined for the six vibrations assigned to the CH2 antisymmetric stretching, CH2 symmetric stretching, CH2 scissoring, C=O stretching, PO2- antisymmetric stretching, and C-C-N+ antisymmetric stretching modes. The results indicate that hydrocarbon chains are inclined at about 75 degrees to the film plane and the polar groups orient parallel to the plane in the builtup film. A structural model of the phosphatidylethanolamine in the built-up film is proposed.

Membranes↗